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Hi,
```
version: v3.0.1
Files and parameters used:
-e 3000000000
-k 31
-o index/processed
-r chm13v2.0.fa
-t 10
-v merged.sorted.multi.vcf
Determine allele se…
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Hi,
First, thanks for developing updog!
I'd like to use the results from updog with another software, Entropy (https://bitbucket.org/buerklelab/mixedploidy-entropy/), which needs phred-scaled ge…
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While most human population genomics datasets are now able to achieve >30x sequencing coverage on the regular, for a lot of non-model organism studies its becoming more popular to instead use low-cove…
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Hi,
After searching document and issues, I still not sure two things:
1. Is that help to improve imputation accuracy if run GLIMPSE2_phase by multiple samples? I though the GLIMPSE1 algorithm do no…
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This might be a "next release" sort of goal, as it's beyond what we plan for the paper but would nevetheless be helpful.
At the moment we are only calling SNV mutations because that's what our DM mo…
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When processing a BCF file, we can either calculate our own genotype likelihoods from the AD fields, or use the values calculated in a GL or PL field. Creating an option to dng-call and dng-loglike w…
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Hi guys,
currently, `PL` field in the VCF output of SCcaller is defined as follows:
```
##FORMAT=
```
whereas according to [VCF4.3 spec](http://samtools.github.io/hts-specs/VCFv4.3.pdf) it …
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Hi,
I would like to use 'distAngsd-geno' for a large isolation-by-distance analysis in lemurs. I am primarily working with genotype likelihoods estimated with ANGSD. Because I was not sure what in…
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Hello,
I’ve tried with both .bam and .mpileup files but keep getting the following error:
python3.5 Genotype_Likelihoods.py PileupList.txt
Seed is not set.
Default ploidy levels to be tested in…
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Hi Armando,
I'd like to try GONe on a low coverage dataset. I have LD estimates already generated using another program that uses genotype likelihoods for LD estimation from low coverage data. Is the…